Minimizing IL-6 and IL-10 signalling pathway elements using lumping species and parameters

2021 ◽  
Author(s):  
Hemn Mohammed Rasool ◽  
Sarbaz Khoshnaw

Abstract There are many cell signalling pathways that include a higher set of elements. Understanding the dynamics of such systems becomes a difficult issue in systems biology. Mathematical approaches with computational simulations provide a wide range to simplify such complex models and to predicate their dynamics. A powerful technique for reducing the complexity of cell signalling pathways is lumping variables and parameters. In this work, we suggest this technique to reduce the number of elements of IL-6 and IL-10 signalling pathways. The reduced model given in this work provides one a better understanding and predicting some model dynamics, and gives accurate approximate solutions. Computational results show that there is a good agreement between the model dynamics for the original and the simplified models.

2015 ◽  
Vol 137 (12) ◽  
Author(s):  
Philipp Berg ◽  
Christoph Roloff ◽  
Oliver Beuing ◽  
Samuel Voss ◽  
Shin-Ichiro Sugiyama ◽  
...  

With the increased availability of computational resources, the past decade has seen a rise in the use of computational fluid dynamics (CFD) for medical applications. There has been an increase in the application of CFD to attempt to predict the rupture of intracranial aneurysms, however, while many hemodynamic parameters can be obtained from these computations, to date, no consistent methodology for the prediction of the rupture has been identified. One particular challenge to CFD is that many factors contribute to its accuracy; the mesh resolution and spatial/temporal discretization can alone contribute to a variation in accuracy. This failure to identify the importance of these factors and identify a methodology for the prediction of ruptures has limited the acceptance of CFD among physicians for rupture prediction. The International CFD Rupture Challenge 2013 seeks to comment on the sensitivity of these various CFD assumptions to predict the rupture by undertaking a comparison of the rupture and blood-flow predictions from a wide range of independent participants utilizing a range of CFD approaches. Twenty-six groups from 15 countries took part in the challenge. Participants were provided with surface models of two intracranial aneurysms and asked to carry out the corresponding hemodynamics simulations, free to choose their own mesh, solver, and temporal discretization. They were requested to submit velocity and pressure predictions along the centerline and on specified planes. The first phase of the challenge, described in a separate paper, was aimed at predicting which of the two aneurysms had previously ruptured and where the rupture site was located. The second phase, described in this paper, aims to assess the variability of the solutions and the sensitivity to the modeling assumptions. Participants were free to choose boundary conditions in the first phase, whereas they were prescribed in the second phase but all other CFD modeling parameters were not prescribed. In order to compare the computational results of one representative group with experimental results, steady-flow measurements using particle image velocimetry (PIV) were carried out in a silicone model of one of the provided aneurysms. Approximately 80% of the participating groups generated similar results. Both velocity and pressure computations were in good agreement with each other for cycle-averaged and peak-systolic predictions. Most apparent “outliers” (results that stand out of the collective) were observed to have underestimated velocity levels compared to the majority of solutions, but nevertheless identified comparable flow structures. In only two cases, the results deviate by over 35% from the mean solution of all the participants. Results of steady CFD simulations of the representative group and PIV experiments were in good agreement. The study demonstrated that while a range of numerical schemes, mesh resolution, and solvers was used, similar flow predictions were observed in the majority of cases. To further validate the computational results, it is suggested that time-dependent measurements should be conducted in the future. However, it is recognized that this study does not include the biological aspects of the aneurysm, which needs to be considered to be able to more precisely identify the specific rupture risk of an intracranial aneurysm.


1999 ◽  
Author(s):  
Valerian Nemchinsky

Abstract The melting rate of a solid, subjected to a heat flux at its surface, changes with time. When a fresh unmelted surface is first exposed to a heat source, the melting isotherm moves quickly inside the solid. Then its motion slows down: this decrease in melting rate is obviously because of increasing thermal resistance of the growing liquid layer that separates solid-liquid interface from the heat source. If the liquid layer is not removed, the melting rate approaches zero. The resultant melting rate depends on the manner in which the melt is removed. In a number of cases of practical interest, the melt is removed not continuously but periodically, in the form of drops. For example, during arc welding with a consumable electrode, these drops are accumulated at the tip of the electrode. When the drop becomes big enough, it is detached from the electrode under action of gravity or electromagnetic force the melt is removed not continuously but periodically, in the form of drops. A simple approximate method is suggested to calculate the melting rate of a solid in the case when melt is removed periodically in form of drops. The method allows one to consider separately the heat transfer in the solid and in the liquid and, thus, to include different heat processes in both phases. Good agreement was demonstrated for exact and approximate solutions for a wide range of parameters.


2020 ◽  
Vol 499 (3) ◽  
pp. 4418-4431 ◽  
Author(s):  
Sujatha Ramakrishnan ◽  
Aseem Paranjape

ABSTRACT We use the Separate Universe technique to calibrate the dependence of linear and quadratic halo bias b1 and b2 on the local cosmic web environment of dark matter haloes. We do this by measuring the response of halo abundances at fixed mass and cosmic web tidal anisotropy α to an infinite wavelength initial perturbation. We augment our measurements with an analytical framework developed in earlier work that exploits the near-lognormal shape of the distribution of α and results in very high precision calibrations. We present convenient fitting functions for the dependence of b1 and b2 on α over a wide range of halo mass for redshifts 0 ≤ z ≤ 1. Our calibration of b2(α) is the first demonstration to date of the dependence of non-linear bias on the local web environment. Motivated by previous results that showed that α is the primary indicator of halo assembly bias for a number of halo properties beyond halo mass, we then extend our analytical framework to accommodate the dependence of b1 and b2 on any such secondary property that has, or can be monotonically transformed to have, a Gaussian distribution. We demonstrate this technique for the specific case of halo concentration, finding good agreement with previous results. Our calibrations will be useful for a variety of halo model analyses focusing on galaxy assembly bias, as well as analytical forecasts of the potential for using α as a segregating variable in multitracer analyses.


1975 ◽  
Vol 21 (12) ◽  
pp. 1754-1760 ◽  
Author(s):  
John A Lott ◽  
Kathie Turner

Abstract Trinder's method for glucose has nearly all the attributes of an ideal automated colorimetric glucose oxidase procedure. The chemicals used in the color reaction with peroxidase are readily available, the solutions are stable and can be prepared by the user, the method is highly specific and largely free of interferences, the sensitivity can be adjusted by the user to cover a wide range of glucose concentrations, and the reagents are not hazardous. We found very good agreement between results by this method and by the hexokinase and Beckman Glucose Analyzer methods. The method has been modified and adapted to the AutoAnalyzer I and SMA 6/60 (Technicon) with manifolds that give very little interaction between specimens. A study of the method by the simplex technique revealed that the glucose oxidase activity in the reagent is the most critical variable.


2000 ◽  
Vol 122 (3) ◽  
pp. 147-152 ◽  
Author(s):  
Hui He ◽  
Mohamad Metghalchi ◽  
James C. Keck

A simple model has been developed to estimate the sensible thermodynamic properties such as Gibbs free energy, enthalpy, heat capacity, and entropy of hydrocarbons over a wide range of temperatures with special attention to the branched molecules. The model is based on statistical thermodynamic expressions incorporating translational, rotational and vibrational motions of the atoms. A method to determine the number of degrees of freedom for different motion modes (bending and torsion) has been established. Branched rotational groups, such as CH3 and OH, have been considered. A modification of the characteristic temperatures for different motion mode has been made which improves the agreement with the exact values for simple cases. The properties of branched alkanes up to 2,3,4,-trimthylpentane have been calculated and the results are in good agreement with the experimental data. A relatively small number of parameters are needed in this model to estimate the sensible thermodynamic properties of a wide range of species. The model may also be used to estimate the properties of molecules and their isomers, which have not been measured, and is simple enough to be easily programmed as a subroutine for on-line kinetic calculations. [S0195-0738(00)00902-X]


VLSI Design ◽  
1998 ◽  
Vol 8 (1-4) ◽  
pp. 355-360 ◽  
Author(s):  
Stephen Bennett ◽  
Christopher M. Snowden ◽  
Stavros Iezekiel

A theoretical (using rate equations) and experimental study of the nonlinear dynamics of a distributed feedback multiple quantum well laser diode is presented. The analysis is performed under direct modulation. Period doubling and period tripling are identified in both the measurements and simulations. Period doubling is found over a wide range of modulation frequencies in the laser. Computational results using rate equations show good agreement with the experimental results.


2014 ◽  
Vol 12 (2) ◽  
pp. 153-163
Author(s):  
Viktor Anishchenko ◽  
Vladimir Rybachenko ◽  
Konstantin Chotiy ◽  
Andrey Redko

AbstractDFT calculations of vibrational spectra of chlorophosphates using wide range of basis sets and hybrid functionals were performed. Good agreement between calculated and experimental vibrational spectra was reached by the combination of non-empirical functional PBE0 with both middle and large basis sets. The frequencies of the stretching vibrations of the phosphate group calculated using semi-empirical functional B3LYP for all basis sets deviate significantly from the experimental values. The number of polarization functions on heavy atoms was shown to be a key factor for the calculation of vibrational frequencies of organophosphates. The importance of consideration of all the stable rotamers for a complete assignment of fundamental modes was shown.


Author(s):  
Anil K. Tolpadi ◽  
Michael E. Crawford

The heat transfer and aerodynamic performance of turbine airfoils are greatly influenced by the gas side surface finish. In order to operate at higher efficiencies and to have reduced cooling requirements, airfoil designs require better surface finishing processes to create smoother surfaces. In this paper, three different cast airfoils were analyzed: the first airfoil was grit blasted and codep coated, the second airfoil was tumbled and aluminide coated, and the third airfoil was polished further. Each of these airfoils had different levels of roughness. The TEXSTAN boundary layer code was used to make predictions of the heat transfer along both the pressure and suction sides of all three airfoils. These predictions have been compared to corresponding heat transfer data reported earlier by Abuaf et al. (1997). The data were obtained over a wide range of Reynolds numbers simulating typical aircraft engine conditions. A three-parameter full-cone based roughness model was implemented in TEXSTAN and used for the predictions. The three parameters were the centerline average roughness, the cone height and the cone-to-cone pitch. The heat transfer coefficient predictions indicated good agreement with the data over most Reynolds numbers and for all airfoils-both pressure and suction sides. The transition location on the pressure side was well predicted for all airfoils; on the suction side, transition was well predicted at the higher Reynolds numbers but was computed to be somewhat early at the lower Reynolds numbers. Also, at lower Reynolds numbers, the heat transfer coefficients were not in very good agreement with the data on the suction side.


2012 ◽  
Vol 598 ◽  
pp. 516-519
Author(s):  
Yu Qing Ding ◽  
Wen Hui Tang ◽  
Xian Wen Ran ◽  
Xin Xu

The computational analysis of plate impact experiments on dry sand utilizing the Mie- Grüneisen (MG) equation of state and the P-α compaction model were investigated in this study. A number of two dimensional axial symmetric computations were performed by using the hydrocode AUTODYN. The computational results were compared with the particle velocity on the back surface of the rear plate measured by the VISAR system and the first shock-wave arrival times detected by piezoelectric pins in the samples respectively. It was found that the P-α compaction model was more accurately reproduce the experimental data than the MG EOS.


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